A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein

Area of Science:

• Biophysics
• Protein Folding
• Molecular Dynamics

Background:

• Knotted proteins are rare but crucial biological molecules.
• Their complex 3D structures (topologies) present unique physical properties.
• Understanding how topology affects protein behavior is essential.

Purpose of the Study:

• To investigate the influence of protein knot topology on physical properties.
• To study electric-field-driven unfolding and translocation of knotted proteins through a model pore.
• To elucidate the mechanism behind unusual translocation behaviors.

Main Methods:

• Single-molecule nanopore experiments.
• All-atom molecular dynamics (MD) simulations.
• Analysis of electric-field-driven translocation dynamics.

Main Results:

• Observed electric-field-driven unfolding and translocation of individual protein knots.
• Identified an unusual translocation behavior in one knot, resembling electron hopping.
• This knot exhibited a "Marcus inverted regime" where translocation rate plateaued or decreased with increased electric potential.

Conclusions:

• Protein topology significantly impacts forced translocation dynamics through nanopores.
• The observed Marcus inverted regime highlights the complex interplay between electric potential, protein knot structure, and translocation kinetics.
• Findings provide insights into the physical behavior of knotted proteins relevant to tRNA methylation.